A search for specificity in DNA-drug interactions.

The GRID force field and a principal component analysis have been used in order to predict the interactions of small chemical groups with all 64 different triplet sequences of B-DNA. Factors that favor binding to guanine-cytosine base pairs have been identified, and a dictionary of ligand groups and their locations is presented as a guide to the design of specific DNA ligands.

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds.

The directional properties of hydrogen bonds play a major role in determining the specificity of intermolecular interactions. An energy function which takes explicit account of these properties has been developed for use in the determination of energetically favorable ligand binding sites on molecules of known structure by the GRID method (Goodford, P.J.J. Med. Chem. 1985, 28, 849. Boobbyer, D.N.A.; Goodford, P.J.; McWhinnie, P.M.; Wade, R.C.J. Med. Chem. 1989, 32, 1083). In this method, the interaction energy between a target molecule and a small chemical group (a probe), which may be part of a larger ligand, was calculated using an energy function consisting of Lennard-Jones, electrostatic, and hydrogen bond terms. The latter term was a function of the length of the hydrogen bond, its orientation at the hydrogen-bonding atoms, and their chemical nature. We now describe hydrogen bond energy functions which take account of the spatial distribution of the hydrogen bonds made by probes with the ability to form two hydrogen bonds. These functions were designed so as to model the experimentally observed angular dependence of the hydrogen bonds. We also describe the procedure to locate the position and orientation of the probe at which the interaction energy is optimized. The use of this procedure is demonstrated by examples of biological and pharmacological interest which show that it can produce results that are consistent with other theoretical approaches and with experimental observations.

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds.

The specificity of interactions between biological macromolecules and their ligands may be partially attributed to the directional properties of hydrogen bonds. We have now extended the GRID method (Goodford, P. J. J. Med. Chem. 1985, 28, 849. Boobbyer, D. N. A.; Goodford, P. J.; McWhinnie, P. M.; Wade, R. C. J. Med. Chem. 1989, 32, 1083), of determining energetically favorable ligand binding sites on molecules of known structure, in order to improve the treatment of groups which can make multiple hydrogen bonds. In this method, the interaction energy between a probe (a small chemical group that may be part of a larger ligand) and a target molecule is calculated using an energy function which includes a hydrogen bond term which is dependent on the length of the hydrogen bond, its orientation at the hydrogen-bonding atoms, and their chemical character. The methods described in the preceding paper (Wade, R. C.; Clark, K. J.; Goodford, P. J. J. Med. Chem., preceding paper in this issue) for probes capable of making two hydrogen bonds are here extended to the following probes which have the ability to make more than two hydrogen bonds: ammonium-NH3+, amine-NH2, sp3-hybridized hydroxyl, and water. Use of the improved GRID procedure is demonstrated by the determination of the conformation of an amino acid side chain at the subunit interface in hemoglobin and of the location of water binding sites in human lysozyme.

Identifying targets for bioreductive agents: using GRID to predict selective binding regions of proteins.

A computational procedure is described for investigating potential binding sites of a target macromolecule for their ability to bind both a reduced probe molecule and an oxidized probe molecule. The interaction energies are obtained using a molecular mechanics method and can be displayed as three-dimensional (3D) energy contours, indicating regions of the target molecule that may have favorable interactions with the probe molecule. Differences in the interaction energies of the oxidized and reduced probe with the target can also be plotted as contours, indicating regions that are selective for the reduced probe. These selectivity contours can be used to show whether the macromolecule is a potential target for bioreductive agents. The method has been applied to the chicken liver dihydrofolate reductase enzyme and has indicated new binding regions that may be suitable binding sites for bioreductive agents.

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure.

An empirical energy function designed to calculate the interaction energy of a chemical probe group, such as a carbonyl oxygen or an amine nitrogen atom, with a target molecule has been developed. This function is used to determine the sites where ligands, such as drugs, may bind to a chosen target molecule which may be a protein, a nucleic acid, a polysaccharide, or a small organic molecule. The energy function is composed of a Lennard-Jones, an electrostatic and a hydrogen-bonding term. The latter is dependent on the length and orientation of the hydrogen bond and also on the chemical nature of the hydrogen-bonding atoms. These terms have been formulated by fitting to experimental observations of hydrogen bonds in crystal structures. In the calculations, thermal motion of the hydrogen-bonding hydrogen atoms and lone-pair electrons may be taken into account. For example, in a alcoholic hydroxyl group, the hydrogen may rotate around the C-O bond at the observed tetrahedral angle. In a histidine residue, a hydrogen atom may be bonded to either of the two imidazole nitrogens and movement of this hydrogen will cause a redistribution of charge which is dependent on the nature of the probe group and the surrounding environment. The shape of some of the energy functions is demonstrated on molecules of pharmacological interest.

The role of hydrogen-bonds in drug binding.

Hydrogen-bonds play a crucial role in determining the specificity of ligand binding. Their important contribution is explicitly incorporated into a computational method, called GRID, which has been designed to detect energetically favourable ligand binding sites on a chosen target molecule of known structure. An empirical energy function consisting of a Lennard-Jones, an electrostatic and a hydrogen-bonding term is employed. The latter term is found to be necessary because spherically symmetric atom-centred forces alone may not adequately reproduce the geometry of two interacting molecules. The hydrogen-bonding term is dependent on the length and orientation of the hydrogen-bond. Its functional form also varies according to the chemical nature of both the hydrogen-bond donor and acceptor atoms, and has been modelled to fit experimental observations of crystal structures. The mobility of the hydrogen-bonding hydrogens is considered analytically in calculating the hydrogen-bond energy. The hydrogen-bonding energy functions will be described and their application will be demonstrated on molecules of pharmacological interest where hydrogen-bonds influence the binding of ligands.

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.

The interaction of a probe group with a protein of known structure is computed at sample positions throughout and around the macromolecule, giving an array of energy values. The probes include water, the methyl group, amine nitrogen, carboxy oxygen, and hydroxyl. Contour surfaces at appropriate energy levels are calculated for each probe and displayed by computer graphics together with the protein structure. Contours at negative energy levels delineate contours also enable other regions of attraction between probe and protein and are found at known ligand binding clefts in particular. The contours also enable other regions of attraction to be identified and facilitate the interpretation of protein-ligand energetics. They may, therefore, be of value for drug design.

Substituted benzaldehydes designed to increase the oxygen affinity of human haemoglobin and inhibit the sickling of sickle erythrocytes.

Substituted benzaldehydes have been designed to bind preferentially to the oxy conformation of human haemoglobin at a site between the amino terminal residues of the alpha-subunits. Such compounds should stabilize the oxygenated form of haemoglobin and thereby increase its oxygen affinity. The compounds produce the expected effect, left-shifting the oxygen saturation curve of dilute haemoglobin solutions and of whole blood, although the binding pattern to haemoglobin is more complex than envisaged by the design hypothesis. The predicted best compound is also a potent inhibitor, at low oxygen pressure, of the sickling of erythrocytes from patients homozygous for sickle cell disease, and may prove to be a clinically useful anti-sickling agent.

The interaction of human haemoglobin with allosteric effectors as a model for drug-receptor interactions.

1 The release of bound oxygen from oxyhaemoglobin by allosteric effectors is considered as a model for those drug-receptor interactions where the primary response to agonist binding is the release of a second messenger species. 2 A theory of haemoglobin oxygenation, based on the two-state model of Monod, Wyman & Changeux (1965) is used to predict the relationship between 'pharmacological' response and dose of agonist. This relationship is the same as that derived from classical pharmacological occupancy theory. 3 The potency of an agonist is a weighted average of its affinities for the two conformational states of the receptor. 4 The efficacy of an agonist depends not only upon its binding to one of the two conformational states, but also on its ability to alter the functional properties of that state by lowering the affinity of the state for the second messenger. 5 2,3-Diphosphoglycerate and adenosine triphosphate are approximately equipotent and of similar efficacy, but inositol hexaphosphate is about 500 times more potent and has a higher efficacy.

Species differences in the binding of compounds designed to fit a site of known structure in adult human haemoglobin.

1. Oxygen dissociation curves are reported for human haemoglobins A1, FII, FI, A1c and Raleigh (beta1 valine leads to acetylalanine) and for horse haemoglobin in the absence and presence of 2,3-diphosphoglycerate (DPG), or 4,4'-diformyl-2-bibenzyl oxyacetic acid, or the bisulphite addition compound of the latter. 2. These haemoglobins were selected because their amino acid sequences are different at the DPG receptor site of human adult deoxyhaemoglobin. 3. The size of the shifts of the dissociation curves are in the sequence expected from the postulated numbers of interactions made by each compound with each haemoglobin type, based on the assumption of a common receptor site for the three compounds. 4. Multiple linear regression analysis shows that the free energies of interaction of the compounds with the haemoglobins may be predicted, to a first approximation, by summing the number of ionic and covalent bonds predicted for each effector-receptor combination, a reversible covalent bond contributing about twice as much energy (-6.78 kJmol-1) as an ionic interaction (-3.14 kJmol-1).

A quantitative analysis of the effects of 2,3-diphosphoglycerate, adenosine triphosphate and inositol hexaphosphate on the oxygen dissociation curve of human haemoglobin.

1. Oxygen dissociation curves have been measured for human haemoglobin solutions with different concentrations of the allosteric effectors 2,3-diphosphoglycerate, adenosine triphosphate and inositol hexaphosphate. 2. Each effector produces a concentration dependent right shift of the oxygen dissociation curve, but a point is reached where the shift is maximal and increasing the effector concentration has no further effect. 3. Mathematical models based on the Monod, Wyman & Changeux (1965) treatment of allosteric proteins have been fitted to the data. For each compound the simple two-state model and its extension to take account of subunit inequivalence were shown to be inadequate, and a better fit was obtained by allowing the effector to lower the oxygen affinity of the deoxy conformational state as well as binding preferentially to this conformation.

The effect of 2,3-diphosphoglycerate on the oxygen dissociation curve of human haemoglobin.

1. Oxygen dissociation curves for concentrated human haemoglobin solutions (1.6 mmol dm-3 in haem) have been measured by mixing known quantities of oxy- and deoxyhaemoglobin solutions and measuring the resulting partial pressure of oxygen with an oxygen electrode. 2. Observations in the presence of 2,3-diphosphoglycerate support previous conclusions derived from experiments at low haemoglobin concentrations, the validity of which has been questioned. 3. The two affinity state model of Monod, Wyman & Changeux (1965) does not fully describe the actions of 2,3-diphosphoglycerate and a model in which this allosteric effector not only binds preferentially to the T state but also lowers the oxygen affinity of this state gives an improved fit to the data.

The interaction of some bis-arylhydroxysulphonic acids with a site of known structure in human haemoglobin.

1 Two bis-arylhydroxysulphonic acids were previously designed to interact with the known molecular configuration of the 2,3-diphosphoglycerate (DPG) receptor-site of human haemoglobin. These compounds liberate oxygen from the haemoglobin similarly to DPG. 2 Solutions of haemoglobin have now been observed under physiological conditions by nuclear magnetic resonance (n.m.r.) in the presence of DPG and of the compounds. 3 Two peaks in the n.m.r. spectrum of haemoglobin are shifted when DPG is added to the solution. 4 The same two peaks in the spectrum are affected by the compounds. 5 The observations are compatible with the predicted interaction between the compounds and the haemoglobin receptor site.

Symmetry in prostaglandins.

Observations of the agonist activity of prostaglandins on the guinea-pig ileum are analysed. The structure-activity relationships are interpreted in relation to the approximate diad axis of symmetry in the molecules. It is suggested that some receptors for prostaglandins may have a perfect diad axis of symmetry between identical protein subunits.